scripts/Overlap.veryshort.sh
#!/bin/bash
humanRef=$1
File=$2
FinalCoverage=$3
NameStub=$4.V2
HashList=$5
HashSize=$6
Threads=$7
MaxAlleleSize=$8

SampleJhash=$9
ParentsJhash=${10}

humanRefBwa=${11}
refHash=${12}
MaxCov=100000
echo " you gave
File=$2
FinalCoverage=$3
NameStub=$4.V2
HashList=$5
HashSize=$6
Threads=$7
"

echo "final coveage is $FinalCoverage"


echo "RUNNING THIS ONE"
echo "@@@@@@@@@@@@@__IN_OVERLAP__@@@@@@@@@@@@@@@"
echo "human ref in Overlap is $humanRef"
echo "bwa human ref in Overlap is $humanRefBwa"
echo "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
mkdir ./TempOverlap/
mkdir ./Intermediates/
echo "Overlaping $File"

CDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"


RDIR=$CDIR/../

OverlapHash=$RDIR/bin/Overlap
OverlapRebion2=$RDIR/bin/OverlapRegion
ReplaceQwithDinFASTQD=$RDIR/bin/ReplaceQwithDinFASTQD
ConvertFASTqD=$RDIR/bin/ConvertFASTqD.to.FASTQ
AnnotateOverlap=$RDIR/bin/AnnotateOverlap
bwa=$RDIR/bin/externals/bwa/src/bwa_project/bwa
RUFUSinterpret=$RDIR/bin/RUFUS.interpret
CheckHash=$RDIR/scripts/CheckJellyHashList.sh
OverlapSam=$RDIR/bin/OverlapSam
JellyFish=$RDIR/bin/externals/jellyfish/src/jellyfish_project/bin/jellyfish
MOBList=$RDIR/resources/primate_non-LTR_Retrotransposon.fasta

#if [ -s $NameStub.overlap.hashcount.fastq ]
#then 
#	echo "Skipping Overlap"
#else


#if [ -s ./$File.bam ] 
#then 
	echo "skipping align"
#else
#	$bwa mem -t $Threads $humanRefBwa "$File" | samtools sort -T $File -O bam - > $File.bam
#	samtools index $File.bam 
#fi

if [ -s ./TempOverlap/$NameStub.sam.fastqd ]
then
        echo "skipping sam assemble"
else

        $OverlapSam <( samtools view  -F 3328 $File.bam | awk '$9 > 100 || $9 < -100 || $9==0' ) .99 20 $FinalCoverage ./TempOverlap/$NameStub.sam $NameStub 1 $HashList $Threads
fi
if [ -s ./$NameStub.overlap.hashcount.fastq ]
then
        echo "skipping final overlap work"
else

        $ReplaceQwithDinFASTQD ./TempOverlap/$NameStub.sam.fastqd > ./$NameStub.overlap.fastqd
        $ConvertFASTqD ./$NameStub.overlap.fastqd > ./$NameStub.overlap.fastq

        echo "$AnnotateOverlap $HashList ./$NameStub.overlap.fastq TempOverlap/$NameStub.overlap.asembly.hash.fastq > ./$NameStub.overlap.hashcount.fastq"              
              $AnnotateOverlap $HashList ./$NameStub.overlap.fastq TempOverlap/$NameStub.overlap.asembly.hash.fastq > ./$NameStub.overlap.hashcount.fastq
fi

if [ -s ./$NameStub.overlap.hashcount.fastq.bam ]
then 
	echo "skipping contig alignment" 
else
        $bwa mem -t $Threads -Y -E 0,0 -O 6,6  -d 500 -w 500 -L 0,0 $humanRefBwa ./$NameStub.overlap.hashcount.fastq | samtools sort -T $File -O bam - > ./$NameStub.overlap.hashcount.fastq.bam
	samtools index ./$NameStub.overlap.hashcount.fastq.bam
fi

if [ -s ./TempOverlap/$NameStub.overlap.hashcount.fastq.MOB.sam ]
then
	echo "skipping MOB alignemnt check "
else 
	$bwa mem -t $Threads -Y -E 0,0 -O 6,6  -d 500 -w 500 -L 0,0 $MOBList ./$NameStub.overlap.hashcount.fastq | samtools sort -T $File -O sam - > ./TempOverlap/$NameStub.overlap.hashcount.fastq.MOB.sam
fi 


#############################################################################################################
if [ -e ./Intermediates/$NameStub.overlap.asembly.hash.fastq.ref.fastq ]
then 
	echo "skipping pull reference sequecnes"
else

	$RDIR/bin/externals/bedtools2/src/bedtools2_project/bin/fastaFromBed -bed <( $RDIR/bin/externals/bedtools2/src/bedtools2_project/bin/bamToBed -i ./$NameStub.overlap.hashcount.fastq.bam |  awk '{s=$2-100; if (s<0) {print $1 "\t" 0  "\t" $3+100} else {print $1 "\t" s  "\t" $3+100}}'  ) -fi $humanRef -fo ./Intermediates/$NameStub.overlap.asembly.hash.fastq.ref.fastq 

fi 

if [ -e ./Intermediates/$NameStub.overlap.hashcount.fastq.Jhash ]
then 
	echo "skipping var hash generationr"
else
	echo "$JellyFish count -m $HashSize -s 1G -t 20 -o ./Intermediates/$NameStub.overlap.hashcount.fastq.Jhash ./$NameStub.overlap.hashcount.fastq"
	$JellyFish count -m $HashSize -s 1G -t 20 -o ./Intermediates/$NameStub.overlap.hashcount.fastq.Jhash ./$NameStub.overlap.hashcount.fastq
	echo "$JellyFish dump  -c ./Intermediates/$NameStub.overlap.hashcount.fastq.Jhash > ./Intermediates/$NameStub.overlap.hashcount.fastq.Jhash.tab"
	$JellyFish dump  -c ./Intermediates/$NameStub.overlap.hashcount.fastq.Jhash > ./Intermediates/$NameStub.overlap.hashcount.fastq.Jhash.tab
fi 

if [ -s ./Intermediates/$NameStub.overlap.asembly.hash.fastq.ref.fastq.Jhash ] 
then 
	echo "skipping ref hash generation"
else
	$JellyFish count -m $HashSize -s 1G -t 20 -o ./Intermediates/$NameStub.overlap.asembly.hash.fastq.ref.fastq.Jhash ./Intermediates/$NameStub.overlap.asembly.hash.fastq.ref.fastq
	$JellyFish dump -c  ./Intermediates/$NameStub.overlap.asembly.hash.fastq.ref.fastq.Jhash > ./Intermediates/$NameStub.overlap.asembly.hash.fastq.ref.fastq.Jhash.tab
fi
 
if [ -s Intermediates/$NameStub.overlap.asembly.hash.fastq.sample ]
then
        echo "skipping  Intermediates/$NameStub.overlap.asembly.hash.fastq.sample file already exitst"
else
	echo "starting hash lookup this one"
        bash $CheckHash $SampleJhash ./Intermediates/$NameStub.overlap.hashcount.fastq.Jhash.tab 0 $MaxCov> Intermediates/$NameStub.overlap.asembly.hash.fastq.sample
	echo "done with hash lookup"
fi
for parent in $ParentsJhash
        do
            if [ -s Intermediates/$NameStub.overlap.asembly.hash.fastq.$parent ]
            then
                echo "skiping Intermediates/$NameStub.overlap.asembly.hash.fastq.$parent already exists"
            else
                bash $CheckHash $parent ./Intermediates/$NameStub.overlap.hashcount.fastq.Jhash.tab 0 $MaxCov> Intermediates/$NameStub".overlap.asembly.hash.fastq."$parent
            fi
done



if [ -s Intermediates/$NameStub.overlap.asembly.hash.fastq.Ref.sample ]	
then 
	echo "skipping Intermediates/$NameStub.overlap.asembly.hash.fastq.Ref.sample"
else
	bash $CheckHash $SampleJhash  ././Intermediates/$NameStub.overlap.asembly.hash.fastq.ref.fastq.Jhash.tab 0 $MaxCov> Intermediates/$NameStub.overlap.asembly.hash.fastq.Ref.sample
fi

for parent in $ParentsJhash
do
    if [ -s ./Intermediates/$NameStub.overlap.asembly.hash.fastq.Ref.$parent ]
    then
        echo "skipping $NameStub.overlap.asembly.hash.fastq.Ref.$parent already exitst"
    else
	
        #echo "-$parent-"
        #echo " bash $CheckHash $parent ./$NameStub.overlap.asembly.hash.fastq.ref.fastq.Jhash.tab 0 $MaxCov> $NameStub.overlap.asembly.hash.fastq.Ref.$parent"
        bash $CheckHash $parent ./Intermediates/$NameStub.overlap.asembly.hash.fastq.ref.fastq.Jhash.tab 0 $MaxCov> ./Intermediates/$NameStub.overlap.asembly.hash.fastq.Ref.$parent
    fi
done

parentCRString=""
c="-c"
cr="-cR"
space=" "


######################## BUILDING UP parent c and cR string ##############################
for parent in $ParentsJhash;
do
    parentCRString="$parentCRString -c ./Intermediates/$NameStub.overlap.asembly.hash.fastq.$parent -cR ./Intermediates/$NameStub.overlap.asembly.hash.fastq.Ref.$parent "
done

#echo "final parent String is  $parentCRString"
##########################################################################################

if [ -s ./Intermediates/$NameStub.ref.RepRefHash ]
then
        echo "Exclude already exists"
else
	echo "bash $CheckHash $refHash ./Intermediates/$NameStub.overlap.hashcount.fastq.Jhash.tab 0 $MaxCov > Intermediates/$NameStub.ref.RepRefHash"
	bash $CheckHash $refHash ./Intermediates/$NameStub.overlap.hashcount.fastq.Jhash.tab 0 $MaxCov> Intermediates/$NameStub.ref.RepRefHash
fi
wait

mkfifo check 
samtools index ./$NameStub.overlap.hashcount.fastq.bam

echo "$RUFUSinterpret -mob ./TempOverlap/$NameStub.overlap.hashcount.fastq.MOB.sam  -mod Intermediates/$NameStub.overlap.asembly.hash.fastq.sample -mQ 8 -r $humanRef -hf $HashList -o  ./$NameStub.overlap.hashcount.fastq.bam -m $MaxAlleleSize $(echo $parentCRString) -sR Intermediates/$NameStub.overlap.asembly.hash.fastq.Ref.sample -s Intermediates/$NameStub.overlap.asembly.hash.fastq.sample -e ./Intermediates/$NameStub.ref.RepRefHash "





samtools view ./$NameStub.overlap.hashcount.fastq.bam | $RUFUSinterpret -mob ./Intermediates/$NameStub.overlap.hashcount.fastq.MOB.sam -mod Intermediates/$NameStub.overlap.asembly.hash.fastq.sample -mQ 1 -r $humanRef -hf $HashList -o  ./$NameStub.overlap.hashcount.fastq.bam -m $MaxAlleleSize $(echo $parentCRString) -sR Intermediates/$NameStub.overlap.asembly.hash.fastq.Ref.sample -s Intermediates/$NameStub.overlap.asembly.hash.fastq.sample -e ./Intermediates/$NameStub.ref.RepRefHash 


